Commit ad33c271 authored by Peter van 't Hof's avatar Peter van 't Hof

Added centrifuge to report

parent 39647fd4
...@@ -10,11 +10,12 @@ ...@@ -10,11 +10,12 @@
<%@ var libId: Option[String] = None %> <%@ var libId: Option[String] = None %>
<%@ var args: Map[String, Any] %> <%@ var args: Map[String, Any] %>
<%@ var outputDir: File %> <%@ var outputDir: File %>
<%@ var summaryTag: String = "krakenreport" %>
<% <%
val summaries = if (sampleId.isEmpty && libId.isEmpty) { val summaries = if (sampleId.isEmpty && libId.isEmpty) {
summary.getSampleValues("gearskraken", "stats", "krakenreport").map(x => x._1 -> x._2.get.asInstanceOf[Map[String, Any]]) summary.getSampleValues("gearskraken", "stats", summaryTag).map(x => x._1 -> x._2.get.asInstanceOf[Map[String, Any]])
} else summary.getValue(sampleId, libId, "gearskraken", "stats", "krakenreport").map(sampleId.get -> _.asInstanceOf[Map[String, Any]]).toList.toMap } else summary.getValue(sampleId, libId, "gearskraken", "stats", summaryTag).map(sampleId.get -> _.asInstanceOf[Map[String, Any]]).toList.toMap
val tempFile = File.createTempFile("krona.", ".xml") val tempFile = File.createTempFile("krona.", ".xml")
tempFile.deleteOnExit() tempFile.deleteOnExit()
......
...@@ -44,7 +44,7 @@ class GearsCentrifuge(val root: Configurable) extends QScript with SummaryQScrip ...@@ -44,7 +44,7 @@ class GearsCentrifuge(val root: Configurable) extends QScript with SummaryQScrip
krakenReportJSON.output = new File(outputDir, s"$outputName.krkn.json") krakenReportJSON.output = new File(outputDir, s"$outputName.krkn.json")
krakenReportJSON.skipNames = config("skipNames", default = false) krakenReportJSON.skipNames = config("skipNames", default = false)
add(krakenReportJSON) add(krakenReportJSON)
addSummarizable(krakenReportJSON, "centrifugereport") addSummarizable(krakenReportJSON, "centrifuge_report")
addSummaryJobs() addSummaryJobs()
} }
......
...@@ -38,13 +38,17 @@ object GearsReport extends MultisampleReportBuilder { ...@@ -38,13 +38,17 @@ object GearsReport extends MultisampleReportBuilder {
def indexPage = { def indexPage = {
val krakenExecuted = summary.getSampleValues("gearskraken", "stats", "krakenreport").values.forall(_.isDefined) val krakenExecuted = summary.getSampleValues("gearskraken", "stats", "krakenreport").values.forall(_.isDefined)
val centrifugeExecuted = summary.getSampleValues("gearskraken", "stats", "centrifuge_report").values.forall(_.isDefined)
val qiimeClosesOtuTable = summary.getValue("gears", "files", "pipeline", "qiime_closed_otu_table", "path") val qiimeClosesOtuTable = summary.getValue("gears", "files", "pipeline", "qiime_closed_otu_table", "path")
.map(x => new File(x.toString)) .map(x => new File(x.toString))
val qiimeOpenOtuTable = summary.getValue("gears", "files", "pipeline", "qiime_open_otu_table", "path") val qiimeOpenOtuTable = summary.getValue("gears", "files", "pipeline", "qiime_open_otu_table", "path")
.map(x => new File(x.toString)) .map(x => new File(x.toString))
ReportPage( ReportPage(
(if (krakenExecuted) List("Kraken analysis" -> ReportPage(List(), List( (if (centrifugeExecuted) List("Centriguge analysis" -> ReportPage(List(), List(
"Krona plot" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
)), Map("summaryTag" -> "centriguge_report")))
else Nil) ::: (if (krakenExecuted) List("Kraken analysis" -> ReportPage(List(), List(
"Krona plot" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp" "Krona plot" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
)), Map())) )), Map()))
else Nil) ::: (if (qiimeClosesOtuTable.isDefined) List("Qiime closed reference analysis" -> ReportPage(List(), List( else Nil) ::: (if (qiimeClosesOtuTable.isDefined) List("Qiime closed reference analysis" -> ReportPage(List(), List(
......
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